src/samtools/razf.c
5bb21ad5
 /*
  * RAZF : Random Access compressed(Z) File
  * Version: 1.0
  * Release Date: 2008-10-27
  *
  * Copyright 2008, Jue Ruan <ruanjue@gmail.com>, Heng Li <lh3@sanger.ac.uk>
  *
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions
  * are met:
  * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the distribution.
  *
  * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
  * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
  * ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
  * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
  * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
  * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
  * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
  * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
  * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  * SUCH DAMAGE.
  */
 
 #ifndef _NO_RAZF
 
 #include <fcntl.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <unistd.h>
 #include "razf.h"
 
 
 #if ZLIB_VERNUM < 0x1221
 struct _gz_header_s {
     int     text;
     uLong   time;
     int     xflags;
     int     os;
     Bytef   *extra;
     uInt    extra_len;
     uInt    extra_max;
     Bytef   *name;
     uInt    name_max;
     Bytef   *comment;
     uInt    comm_max;
     int     hcrc;
     int     done;
 };
 #warning "zlib < 1.2.2.1; RAZF writing is disabled."
 #endif
 
 #define DEF_MEM_LEVEL 8
 
 static inline uint32_t byte_swap_4(uint32_t v){
 	v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
 	return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
 }
 
 static inline uint64_t byte_swap_8(uint64_t v){
 	v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
 	v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
 	return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
 }
 
 static inline int is_big_endian(){
 	int x = 0x01;
 	char *c = (char*)&x;
 	return (c[0] != 0x01);
 }
 
 #ifndef _RZ_READONLY
 static void add_zindex(RAZF *rz, int64_t in, int64_t out){
 	if(rz->index->size == rz->index->cap){
 		rz->index->cap = rz->index->cap * 1.5 + 2;
 		rz->index->cell_offsets = realloc(rz->index->cell_offsets, sizeof(int) * rz->index->cap);
 		rz->index->bin_offsets  = realloc(rz->index->bin_offsets, sizeof(int64_t) * (rz->index->cap/RZ_BIN_SIZE + 1));
 	}
 	if(rz->index->size % RZ_BIN_SIZE == 0) rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE] = out;
 	rz->index->cell_offsets[rz->index->size] = out - rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE];
 	rz->index->size ++;
 }
 
 static void save_zindex(RAZF *rz, int fd){
 	int32_t i, v32;
 	int is_be;
 	is_be = is_big_endian();
 	if(is_be) write(fd, &rz->index->size, sizeof(int));
 	else {
 		v32 = byte_swap_4((uint32_t)rz->index->size);
 		write(fd, &v32, sizeof(uint32_t));
 	}
 	v32 = rz->index->size / RZ_BIN_SIZE + 1;
 	if(!is_be){
 		for(i=0;i<v32;i++) rz->index->bin_offsets[i]  = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
 		for(i=0;i<rz->index->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]);
 	}
 	write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
 	write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
 }
 #endif
 
 #ifdef _USE_KNETFILE
 static void load_zindex(RAZF *rz, knetFile *fp){
 #else
 static void load_zindex(RAZF *rz, int fd){
 #endif
 	int32_t i, v32;
 	int is_be;
 	if(!rz->load_index) return;
 	if(rz->index == NULL) rz->index = malloc(sizeof(ZBlockIndex));
 	is_be = is_big_endian();
 #ifdef _USE_KNETFILE
 	knet_read(fp, &rz->index->size, sizeof(int));
 #else
 	read(fd, &rz->index->size, sizeof(int));
 #endif
 	if(!is_be) rz->index->size = byte_swap_4((uint32_t)rz->index->size);
 	rz->index->cap = rz->index->size;
 	v32 = rz->index->size / RZ_BIN_SIZE + 1;
 	rz->index->bin_offsets  = malloc(sizeof(int64_t) * v32);
 #ifdef _USE_KNETFILE
 	knet_read(fp, rz->index->bin_offsets, sizeof(int64_t) * v32);
 #else
 	read(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
 #endif
 	rz->index->cell_offsets = malloc(sizeof(int) * rz->index->size);
 #ifdef _USE_KNETFILE
 	knet_read(fp, rz->index->cell_offsets, sizeof(int) * rz->index->size);
 #else
 	read(fd, rz->index->cell_offsets, sizeof(int) * rz->index->size);
 #endif
 	if(!is_be){
 		for(i=0;i<v32;i++) rz->index->bin_offsets[i] = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
 		for(i=0;i<rz->index->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]);
 	}
 }
 
 #ifdef _RZ_READONLY
 static RAZF* razf_open_w(int fd)
 {
 	fprintf(stderr, "[razf_open_w] Writing is not available with zlib ver < 1.2.2.1\n");
 	return 0;
 }
 #else
 static RAZF* razf_open_w(int fd){
 	RAZF *rz;
 #ifdef _WIN32
 	setmode(fd, O_BINARY);
 #endif
 	rz = calloc(1, sizeof(RAZF));
 	rz->mode = 'w';
 #ifdef _USE_KNETFILE
     rz->x.fpw = fd;
 #else
 	rz->filedes = fd;
 #endif
 	rz->stream = calloc(sizeof(z_stream), 1);
 	rz->inbuf  = malloc(RZ_BUFFER_SIZE);
 	rz->outbuf = malloc(RZ_BUFFER_SIZE);
 	rz->index = calloc(sizeof(ZBlockIndex), 1);
 	deflateInit2(rz->stream, RZ_COMPRESS_LEVEL, Z_DEFLATED, WINDOW_BITS + 16, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY);
 	rz->stream->avail_out = RZ_BUFFER_SIZE;
 	rz->stream->next_out  = rz->outbuf;
 	rz->header = calloc(sizeof(gz_header), 1);
 	rz->header->os    = 0x03; //Unix
 	rz->header->text  = 0;
 	rz->header->time  = 0;
 	rz->header->extra = malloc(7);
 	strncpy((char*)rz->header->extra, "RAZF", 4);
 	rz->header->extra[4] = 1; // obsolete field
 	// block size = RZ_BLOCK_SIZE, Big-Endian
 	rz->header->extra[5] = RZ_BLOCK_SIZE >> 8;
 	rz->header->extra[6] = RZ_BLOCK_SIZE & 0xFF;
 	rz->header->extra_len = 7;
 	rz->header->name = rz->header->comment  = 0;
 	rz->header->hcrc = 0;
 	deflateSetHeader(rz->stream, rz->header);
 	rz->block_pos = rz->block_off = 0;
 	return rz;
 }
 
 static void _razf_write(RAZF* rz, const void *data, int size){
 	int tout;
 	rz->stream->avail_in = size;
 	rz->stream->next_in  = (void*)data;
 	while(1){
 		tout = rz->stream->avail_out;
 		deflate(rz->stream, Z_NO_FLUSH);
 		rz->out += tout - rz->stream->avail_out;
 		if(rz->stream->avail_out) break;
 #ifdef _USE_KNETFILE
 		write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
 #else
 		write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
 #endif
 		rz->stream->avail_out = RZ_BUFFER_SIZE;
 		rz->stream->next_out  = rz->outbuf;
 		if(rz->stream->avail_in == 0) break;
 	};
 	rz->in += size - rz->stream->avail_in;
 	rz->block_off += size - rz->stream->avail_in;
 }
 
 static void razf_flush(RAZF *rz){
 	uint32_t tout;
 	if(rz->buf_len){
 		_razf_write(rz, rz->inbuf, rz->buf_len);
 		rz->buf_off = rz->buf_len = 0;
 	}
 	if(rz->stream->avail_out){
 #ifdef _USE_KNETFILE    
 		write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
 #else        
 		write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
 #endif
 		rz->stream->avail_out = RZ_BUFFER_SIZE;
 		rz->stream->next_out  = rz->outbuf;
 	}
 	while(1){
 		tout = rz->stream->avail_out;
 		deflate(rz->stream, Z_FULL_FLUSH);
 		rz->out += tout - rz->stream->avail_out;
 		if(rz->stream->avail_out == 0){
 #ifdef _USE_KNETFILE    
 			write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
 #else            
 			write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
 #endif
 			rz->stream->avail_out = RZ_BUFFER_SIZE;
 			rz->stream->next_out  = rz->outbuf;
 		} else break;
 	}
 	rz->block_pos = rz->out;
 	rz->block_off = 0;
 }
 
 static void razf_end_flush(RAZF *rz){
 	uint32_t tout;
 	if(rz->buf_len){
 		_razf_write(rz, rz->inbuf, rz->buf_len);
 		rz->buf_off = rz->buf_len = 0;
 	}
 	while(1){
 		tout = rz->stream->avail_out;
 		deflate(rz->stream, Z_FINISH);
 		rz->out += tout - rz->stream->avail_out;
 		if(rz->stream->avail_out < RZ_BUFFER_SIZE){
 #ifdef _USE_KNETFILE        
 			write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
 #else            
 			write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
 #endif
 			rz->stream->avail_out = RZ_BUFFER_SIZE;
 			rz->stream->next_out  = rz->outbuf;
 		} else break;
 	}
 }
 
 static void _razf_buffered_write(RAZF *rz, const void *data, int size){
 	int i, n;
 	while(1){
 		if(rz->buf_len == RZ_BUFFER_SIZE){
 			_razf_write(rz, rz->inbuf, rz->buf_len);
 			rz->buf_len = 0;
 		}
 		if(size + rz->buf_len < RZ_BUFFER_SIZE){
 			for(i=0;i<size;i++) ((char*)rz->inbuf + rz->buf_len)[i] = ((char*)data)[i];
 			rz->buf_len += size;
 			return;
 		} else {
 			n = RZ_BUFFER_SIZE - rz->buf_len;
 			for(i=0;i<n;i++) ((char*)rz->inbuf + rz->buf_len)[i] = ((char*)data)[i];
 			size -= n;
 			data += n;
 			rz->buf_len += n;
 		}
 	}
 }
 
 int razf_write(RAZF* rz, const void *data, int size){
 	int ori_size, n;
 	int64_t next_block;
 	ori_size = size;
 	next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_SIZE;
 	while(rz->in + rz->buf_len + size >= next_block){
 		n = next_block - rz->in - rz->buf_len;
 		_razf_buffered_write(rz, data, n);
 		data += n;
 		size -= n;
 		razf_flush(rz);
 		add_zindex(rz, rz->in, rz->out);
 		next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_SIZE;
 	}
 	_razf_buffered_write(rz, data, size);
 	return ori_size;
 }
 #endif
 
 /* gzip flag byte */
 #define ASCII_FLAG   0x01 /* bit 0 set: file probably ascii text */
 #define HEAD_CRC     0x02 /* bit 1 set: header CRC present */
 #define EXTRA_FIELD  0x04 /* bit 2 set: extra field present */
 #define ORIG_NAME    0x08 /* bit 3 set: original file name present */
 #define COMMENT      0x10 /* bit 4 set: file comment present */
 #define RESERVED     0xE0 /* bits 5..7: reserved */
 
 static int _read_gz_header(unsigned char *data, int size, int *extra_off, int *extra_len){
 	int method, flags, n, len;
 	if(size < 2) return 0;
 	if(data[0] != 0x1f || data[1] != 0x8b) return 0;
 	if(size < 4) return 0;
 	method = data[2];
 	flags  = data[3];
 	if(method != Z_DEFLATED || (flags & RESERVED)) return 0;
 	n = 4 + 6; // Skip 6 bytes
 	*extra_off = n + 2;
 	*extra_len = 0;
 	if(flags & EXTRA_FIELD){
 		if(size < n + 2) return 0;
 		len = ((int)data[n + 1] << 8) | data[n];
 		n += 2;
 		*extra_off = n;
 		while(len){
 			if(n >= size) return 0;
 			n ++;
 			len --;
 		}
 		*extra_len = n - (*extra_off);
 	}
 	if(flags & ORIG_NAME) while(n < size && data[n++]);
 	if(flags & COMMENT) while(n < size && data[n++]);
 	if(flags & HEAD_CRC){
 		if(n + 2 > size) return 0;
 		n += 2;
 	}
 	return n;
 }
 
 #ifdef _USE_KNETFILE
 static RAZF* razf_open_r(knetFile *fp, int _load_index){
 #else
 static RAZF* razf_open_r(int fd, int _load_index){
 #endif
 	RAZF *rz;
 	int ext_off, ext_len;
 	int n, is_be, ret;
 	int64_t end;
 	unsigned char c[] = "RAZF";
 	rz = calloc(1, sizeof(RAZF));
 	rz->mode = 'r';
 #ifdef _USE_KNETFILE
     rz->x.fpr = fp;
 #else
 #ifdef _WIN32
 	setmode(fd, O_BINARY);
 #endif
 	rz->filedes = fd;
 #endif
 	rz->stream = calloc(sizeof(z_stream), 1);
 	rz->inbuf  = malloc(RZ_BUFFER_SIZE);
 	rz->outbuf = malloc(RZ_BUFFER_SIZE);
 	rz->end = rz->src_end = 0x7FFFFFFFFFFFFFFFLL;
 #ifdef _USE_KNETFILE
     n = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
 #else
 	n = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
 #endif
 	ret = _read_gz_header(rz->inbuf, n, &ext_off, &ext_len);
 	if(ret == 0){
 		PLAIN_FILE:
 		rz->in = n;
 		rz->file_type = FILE_TYPE_PLAIN;
 		memcpy(rz->outbuf, rz->inbuf, n);
 		rz->buf_len = n;
 		free(rz->stream);
 		rz->stream = NULL;
 		return rz;
 	}
 	rz->header_size = ret;
 	ret = inflateInit2(rz->stream, -WINDOW_BITS);
 	if(ret != Z_OK){ inflateEnd(rz->stream); goto PLAIN_FILE;}
 	rz->stream->avail_in = n - rz->header_size;
 	rz->stream->next_in  = rz->inbuf + rz->header_size;
 	rz->stream->avail_out = RZ_BUFFER_SIZE;
 	rz->stream->next_out  = rz->outbuf;
 	rz->file_type = FILE_TYPE_GZ;
 	rz->in = rz->header_size;
 	rz->block_pos = rz->header_size;
 	rz->next_block_pos = rz->header_size;
 	rz->block_off = 0;
 	if(ext_len < 7 || memcmp(rz->inbuf + ext_off, c, 4) != 0) return rz;
 	if(((((unsigned char*)rz->inbuf)[ext_off + 5] << 8) | ((unsigned char*)rz->inbuf)[ext_off + 6]) != RZ_BLOCK_SIZE){
 		fprintf(stderr, " -- WARNING: RZ_BLOCK_SIZE is not %d, treat source as gz file.  in %s -- %s:%d --\n", RZ_BLOCK_SIZE, __FUNCTION__, __FILE__, __LINE__);
 		return rz;
 	}
 	rz->load_index = _load_index;
 	rz->file_type = FILE_TYPE_RZ;
 #ifdef _USE_KNETFILE
 	if(knet_seek(fp, -16, SEEK_END) == -1){
 #else
 	if(lseek(fd, -16, SEEK_END) == -1){
 #endif
 		UNSEEKABLE:
 		rz->seekable = 0;
 		rz->index = NULL;
 		rz->src_end = rz->end = 0x7FFFFFFFFFFFFFFFLL;
 	} else {
 		is_be = is_big_endian();
 		rz->seekable = 1;
 #ifdef _USE_KNETFILE
         knet_read(fp, &end, sizeof(int64_t));
 #else
 		read(fd, &end, sizeof(int64_t));
 #endif        
 		if(!is_be) rz->src_end = (int64_t)byte_swap_8((uint64_t)end);
 		else rz->src_end = end;
 
 #ifdef _USE_KNETFILE
 		knet_read(fp, &end, sizeof(int64_t));
 #else
 		read(fd, &end, sizeof(int64_t));
 #endif        
 		if(!is_be) rz->end = (int64_t)byte_swap_8((uint64_t)end);
 		else rz->end = end;
 		if(n > rz->end){
 			rz->stream->avail_in -= n - rz->end;
 			n = rz->end;
 		}
 		if(rz->end > rz->src_end){
 #ifdef _USE_KNETFILE
             knet_seek(fp, rz->in, SEEK_SET);
 #else
 			lseek(fd, rz->in, SEEK_SET);
 #endif
 			goto UNSEEKABLE;
 		}
 #ifdef _USE_KNETFILE
         knet_seek(fp, rz->end, SEEK_SET);
 		if(knet_tell(fp) != rz->end){
 			knet_seek(fp, rz->in, SEEK_SET);
 #else
 		if(lseek(fd, rz->end, SEEK_SET) != rz->end){
 			lseek(fd, rz->in, SEEK_SET);
 #endif
 			goto UNSEEKABLE;
 		}
 #ifdef _USE_KNETFILE
 		load_zindex(rz, fp);
 		knet_seek(fp, n, SEEK_SET);
 #else
 		load_zindex(rz, fd);
 		lseek(fd, n, SEEK_SET);
 #endif
 	}
 	return rz;
 }
 
 #ifdef _USE_KNETFILE
 RAZF* razf_dopen(int fd, const char *mode){
     if (strstr(mode, "r")) fprintf(stderr,"[razf_dopen] implement me\n");
     else if(strstr(mode, "w")) return razf_open_w(fd);
 	return NULL;
 }
 
 RAZF* razf_dopen2(int fd, const char *mode)
 {
     fprintf(stderr,"[razf_dopen2] implement me\n");
     return NULL;
 }
 #else
 RAZF* razf_dopen(int fd, const char *mode){
 	if(strstr(mode, "r")) return razf_open_r(fd, 1);
 	else if(strstr(mode, "w")) return razf_open_w(fd);
 	else return NULL;
 }
 
 RAZF* razf_dopen2(int fd, const char *mode)
 {
 	if(strstr(mode, "r")) return razf_open_r(fd, 0);
 	else if(strstr(mode, "w")) return razf_open_w(fd);
 	else return NULL;
 }
 #endif
 
 static inline RAZF* _razf_open(const char *filename, const char *mode, int _load_index){
 	int fd;
 	RAZF *rz;
 	if(strstr(mode, "r")){
 #ifdef _USE_KNETFILE
         knetFile *fd = knet_open(filename, "r");
         if (fd == 0) {
             fprintf(stderr, "[_razf_open] fail to open %s\n", filename);
             return NULL;
         }
 #else
 #ifdef _WIN32
 		fd = open(filename, O_RDONLY | O_BINARY);
 #else
 		fd = open(filename, O_RDONLY);
 #endif
 #endif
 		if(fd < 0) return NULL;
 		rz = razf_open_r(fd, _load_index);
 	} else if(strstr(mode, "w")){
 #ifdef _WIN32
 		fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC | O_BINARY, 0666);
 #else
 		fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC, 0666);
 #endif
 		if(fd < 0) return NULL;
 		rz = razf_open_w(fd);
 	} else return NULL;
 	return rz;
 }
 
 RAZF* razf_open(const char *filename, const char *mode){
 	return _razf_open(filename, mode, 1);
 }
 
 RAZF* razf_open2(const char *filename, const char *mode){
 	return _razf_open(filename, mode, 0);
 }
 
 int razf_get_data_size(RAZF *rz, int64_t *u_size, int64_t *c_size){
 	int64_t n;
 	if(rz->mode != 'r' && rz->mode != 'R') return 0;
 	switch(rz->file_type){
 		case FILE_TYPE_PLAIN:
 			if(rz->end == 0x7fffffffffffffffLL){
 #ifdef _USE_KNETFILE
 				if(knet_seek(rz->x.fpr, 0, SEEK_CUR) == -1) return 0;
                 n = knet_tell(rz->x.fpr);
 				knet_seek(rz->x.fpr, 0, SEEK_END);
                 rz->end = knet_tell(rz->x.fpr);
 				knet_seek(rz->x.fpr, n, SEEK_SET);
 #else
 				if((n = lseek(rz->filedes, 0, SEEK_CUR)) == -1) return 0;
 				rz->end = lseek(rz->filedes, 0, SEEK_END);
 				lseek(rz->filedes, n, SEEK_SET);
 #endif                
 			}
 			*u_size = *c_size = rz->end;
 			return 1;
 		case FILE_TYPE_GZ:
 			return 0;
 		case FILE_TYPE_RZ:
 			if(rz->src_end == rz->end) return 0;
 			*u_size = rz->src_end;
 			*c_size = rz->end;
 			return 1;
 		default:
 			return 0;
 	}
 }
 
 static int _razf_read(RAZF* rz, void *data, int size){
 	int ret, tin;
 	if(rz->z_eof || rz->z_err) return 0;
 	if (rz->file_type == FILE_TYPE_PLAIN) {
 #ifdef _USE_KNETFILE
 		ret = knet_read(rz->x.fpr, data, size);
 #else
 		ret = read(rz->filedes, data, size);
 #endif        
 		if (ret == 0) rz->z_eof = 1;
 		return ret;
 	}
 	rz->stream->avail_out = size;
 	rz->stream->next_out  = data;
 	while(rz->stream->avail_out){
 		if(rz->stream->avail_in == 0){
 			if(rz->in >= rz->end){ rz->z_eof = 1; break; }
 			if(rz->end - rz->in < RZ_BUFFER_SIZE){
 #ifdef _USE_KNETFILE
 				rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, rz->end -rz->in);
 #else
 				rz->stream->avail_in = read(rz->filedes, rz->inbuf, rz->end -rz->in);
 #endif        
 			} else {
 #ifdef _USE_KNETFILE
 				rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
 #else
 				rz->stream->avail_in = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
 #endif        
 			}
 			if(rz->stream->avail_in == 0){
 				rz->z_eof = 1;
 				break;
 			}
 			rz->stream->next_in = rz->inbuf;
 		}
 		tin = rz->stream->avail_in;
 		ret = inflate(rz->stream, Z_BLOCK);
 		rz->in += tin - rz->stream->avail_in;
 		if(ret == Z_NEED_DICT || ret == Z_MEM_ERROR || ret == Z_DATA_ERROR){
 			fprintf(stderr, "[_razf_read] inflate error: %d %s (at %s:%d)\n", ret, rz->stream->msg ? rz->stream->msg : "", __FILE__, __LINE__);
 			rz->z_err = 1;
 			break;
 		}
 		if(ret == Z_STREAM_END){
 			rz->z_eof = 1;
 			break;
 		}
 		if ((rz->stream->data_type&128) && !(rz->stream->data_type&64)){
 			rz->buf_flush = 1;
 			rz->next_block_pos = rz->in;
 			break;
 		}
 	}
 	return size - rz->stream->avail_out;
 }
 
 int razf_read(RAZF *rz, void *data, int size){
 	int ori_size, i;
 	ori_size = size;
 	while(size > 0){
 		if(rz->buf_len){
 			if(size < rz->buf_len){
 				for(i=0;i<size;i++) ((char*)data)[i] = ((char*)rz->outbuf + rz->buf_off)[i];
 				rz->buf_off += size;
 				rz->buf_len -= size;
 				data += size;
 				rz->block_off += size;
 				size = 0;
 				break;
 			} else {
 				for(i=0;i<rz->buf_len;i++) ((char*)data)[i] = ((char*)rz->outbuf + rz->buf_off)[i];
 				data += rz->buf_len;
 				size -= rz->buf_len;
 				rz->block_off += rz->buf_len;
 				rz->buf_off = 0;
 				rz->buf_len = 0;
 				if(rz->buf_flush){
 					rz->block_pos = rz->next_block_pos;
 					rz->block_off = 0;
 					rz->buf_flush = 0;
 				}
 			}
 		} else if(rz->buf_flush){
 			rz->block_pos = rz->next_block_pos;
 			rz->block_off = 0;
 			rz->buf_flush = 0;
 		}
 		if(rz->buf_flush) continue;
 		rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
 		if((rz->z_eof && rz->buf_len == 0) || rz->z_err) break; /* MTM */
 	}
 	rz->out += ori_size - size;
 	return ori_size - size;
 }
 
 int razf_skip(RAZF* rz, int size){
 	int ori_size;
 	ori_size = size;
 	while(size > 0){
 		if(rz->buf_len){
 			if(size < rz->buf_len){
 				rz->buf_off += size;
 				rz->buf_len -= size;
 				rz->block_off += size;
 				size = 0;
 				break;
 			} else {
 				size -= rz->buf_len;
 				rz->buf_off = 0;
 				rz->buf_len = 0;
 				rz->block_off += rz->buf_len;
 				if(rz->buf_flush){
 					rz->block_pos = rz->next_block_pos;
 					rz->block_off = 0;
 					rz->buf_flush = 0;
 				}
 			}
 		} else if(rz->buf_flush){
 			rz->block_pos = rz->next_block_pos;
 			rz->block_off = 0;
 			rz->buf_flush = 0;
 		}
 		if(rz->buf_flush) continue;
 		rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
 		if((rz->z_eof && rz->buf_len == 0) || rz->z_err) break; /* MTM */
 	}
 	rz->out += ori_size - size;
 	return ori_size - size;
 }
 
 static void _razf_reset_read(RAZF *rz, int64_t in, int64_t out){
 #ifdef _USE_KNETFILE
 	knet_seek(rz->x.fpr, in, SEEK_SET);
 #else
 	lseek(rz->filedes, in, SEEK_SET);
 #endif
 	rz->in  = in;
 	rz->out = out;
 	rz->block_pos = in;
 	rz->next_block_pos = in;
 	rz->block_off = 0;
 	rz->buf_flush = 0;
 	rz->z_eof = rz->z_err = 0;
 	inflateReset(rz->stream);
 	rz->stream->avail_in = 0;
 	rz->buf_off = rz->buf_len = 0;
 }
 
 int64_t razf_jump(RAZF *rz, int64_t block_start, int block_offset){
 	int64_t pos;
 	rz->z_eof = 0;
 	if(rz->file_type == FILE_TYPE_PLAIN){
 		rz->buf_off = rz->buf_len = 0;
 		pos = block_start + block_offset;
 #ifdef _USE_KNETFILE
 		knet_seek(rz->x.fpr, pos, SEEK_SET);
         pos = knet_tell(rz->x.fpr);
 #else
 		pos = lseek(rz->filedes, pos, SEEK_SET);
 #endif
 		rz->out = rz->in = pos;
 		return pos;
 	}
 	if(block_start == rz->block_pos && block_offset >= rz->block_off) {
 		block_offset -= rz->block_off;
 		goto SKIP; // Needn't reset inflate
 	}
 	if(block_start  == 0) block_start = rz->header_size; // Automaticly revist wrong block_start
 	_razf_reset_read(rz, block_start, 0);
 	SKIP:
 	if(block_offset) razf_skip(rz, block_offset);
 	return rz->block_off;
 }
 
 int64_t razf_seek(RAZF* rz, int64_t pos, int where){
 	int64_t idx;
 	int64_t seek_pos, new_out;
 	rz->z_eof = 0;
 	if (where == SEEK_CUR) pos += rz->out;
 	else if (where == SEEK_END) pos += rz->src_end;
 	if(rz->file_type == FILE_TYPE_PLAIN){
 #ifdef _USE_KNETFILE
 		knet_seek(rz->x.fpr, pos, SEEK_SET);
         seek_pos = knet_tell(rz->x.fpr);
 #else
 		seek_pos = lseek(rz->filedes, pos, SEEK_SET);
 #endif
 		rz->buf_off = rz->buf_len = 0;
 		rz->out = rz->in = seek_pos;
 		return seek_pos;
 	} else if(rz->file_type == FILE_TYPE_GZ){
 		if(pos >= rz->out) goto SKIP;
                 /* MTM */
                 fprintf(stderr,
                         ".gz files support sequential access only; uncompress");
                 abort();
 		return rz->out;
 	}
 	if(pos == rz->out) return pos;
 	if(pos > rz->src_end) return rz->out;
 	if(!rz->seekable || !rz->load_index){
 		if(pos >= rz->out) goto SKIP;
 	}
 	idx = pos / RZ_BLOCK_SIZE - 1;
 	seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]);
 	new_out  = (idx + 1) * RZ_BLOCK_SIZE;
 	if(pos > rz->out && new_out <= rz->out) goto SKIP;
 	_razf_reset_read(rz, seek_pos, new_out);
 	SKIP:
 	razf_skip(rz, (int)(pos - rz->out));
 	return rz->out;
 }
 
 uint64_t razf_tell2(RAZF *rz)
 {
 	/*
 	if (rz->load_index) {
 		int64_t idx, seek_pos;
 		idx = rz->out / RZ_BLOCK_SIZE - 1;
 		seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]);
 		if (seek_pos != rz->block_pos || rz->out%RZ_BLOCK_SIZE != rz->block_off)
 			fprintf(stderr, "[razf_tell2] inconsistent block offset: (%lld, %lld) != (%lld, %lld)\n",
 					(long long)seek_pos, (long long)rz->out%RZ_BLOCK_SIZE, (long long)rz->block_pos, (long long) rz->block_off);
 	}
 	*/
 	return (uint64_t)rz->block_pos<<16 | (rz->block_off&0xffff);
 }
 
 int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where)
 {
 	if (where != SEEK_SET) return -1;
 	return razf_jump(rz, voffset>>16, voffset&0xffff);
 }
 
 void razf_close(RAZF *rz){
 	if(rz->mode == 'w'){
 #ifndef _RZ_READONLY
 		razf_end_flush(rz);
 		deflateEnd(rz->stream);
 		razf_flush(rz);                  /* MTM */
 		add_zindex(rz, rz->in, rz->out); /* MTM */
 #ifdef _USE_KNETFILE
 		save_zindex(rz, rz->x.fpw);
 		if(is_big_endian()){
 			write(rz->x.fpw, &rz->in, sizeof(int64_t));
 			write(rz->x.fpw, &rz->out, sizeof(int64_t));
 		} else {
 			uint64_t v64 = byte_swap_8((uint64_t)rz->in);
 			write(rz->x.fpw, &v64, sizeof(int64_t));
 			v64 = byte_swap_8((uint64_t)rz->out);
 			write(rz->x.fpw, &v64, sizeof(int64_t));
 		}
 #else
 		save_zindex(rz, rz->filedes);
 		if(is_big_endian()){
 			write(rz->filedes, &rz->in, sizeof(int64_t));
 			write(rz->filedes, &rz->out, sizeof(int64_t));
 		} else {
 			uint64_t v64 = byte_swap_8((uint64_t)rz->in);
 			write(rz->filedes, &v64, sizeof(int64_t));
 			v64 = byte_swap_8((uint64_t)rz->out);
 			write(rz->filedes, &v64, sizeof(int64_t));
 		}
 #endif
 #endif
 	} else if(rz->mode == 'r'){
 		if(rz->stream) inflateEnd(rz->stream);
 	}
 	if(rz->inbuf) free(rz->inbuf);
 	if(rz->outbuf) free(rz->outbuf);
 	if(rz->header){
 		free(rz->header->extra);
 		free(rz->header->name);
 		free(rz->header->comment);
 		free(rz->header);
 	}
 	if(rz->index){
 		free(rz->index->bin_offsets);
 		free(rz->index->cell_offsets);
 		free(rz->index);
 	}
 	free(rz->stream);
 #ifdef _USE_KNETFILE
     if (rz->mode == 'r')
         knet_close(rz->x.fpr);
     if (rz->mode == 'w')
         close(rz->x.fpw);
 #else
 	close(rz->filedes);
 #endif
 	free(rz);
 }
 
 #endif